{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T05:35:23Z","timestamp":1783748123985,"version":"3.55.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2148,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurate prediction of transcription factor binding motifs that are enriched in a collection of sequences remains a computational challenge. Here we report on GimmeMotifs, a pipeline that incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing (ChIP-seq) data. Similar redundant motifs are compared using the weighted information content (WIC) similarity score and clustered using an iterative procedure. A comprehensive output report is generated with several different evaluation metrics to compare and evaluate the results. Benchmarks show that the method performs well on human and mouse ChIP-seq datasets. GimmeMotifs consists of a suite of command-line scripts that can be easily implemented in a ChIP-seq analysis pipeline.<\/jats:p>\n               <jats:p>Availability: GimmeMotifs is implemented in Python and runs on Linux. The source code is freely available for download at http:\/\/www.ncmls.eu\/bioinfo\/gimmemotifs\/.<\/jats:p>\n               <jats:p>Contact: \u00a0s.vanheeringen@ncmls.ru.nl<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq636","type":"journal-article","created":{"date-parts":[[2010,11,17]],"date-time":"2010-11-17T01:33:59Z","timestamp":1289957639000},"page":"270-271","source":"Crossref","is-referenced-by-count":184,"title":["GimmeMotifs: a <i>de novo<\/i> motif prediction pipeline for ChIP-sequencing experiments"],"prefix":"10.1093","volume":"27","author":[{"given":"Simon J.","family":"van Heeringen","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gert Jan C.","family":"Veenstra","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,11,15]]},"reference":[{"issue":"suppl. 2","key":"2023012512173119100_B1","doi-asserted-by":"crossref","first-page":"W259","DOI":"10.1093\/nar\/gkm310","article-title":"SCOPE: a web server for practical de novo motif discovery","volume":"35","author":"Carlson","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512173119100_B2","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1093\/bioinformatics\/19.2.212","article-title":"Rank order metrics for quantifying the association of sequence features with gene regulation","volume":"19","author":"Clarke","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012512173119100_B3","doi-asserted-by":"crossref","first-page":"4899","DOI":"10.1093\/nar\/gki791","article-title":"Limitations and potentials of current motif discovery algorithms","volume":"33","author":"Hu","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012512173119100_B4","doi-asserted-by":"crossref","first-page":"3191","DOI":"10.1093\/bioinformatics\/btp570","article-title":"W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data","volume":"25","author":"Jin","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512173119100_B5","doi-asserted-by":"crossref","first-page":"e1001065","DOI":"10.1371\/journal.pgen.1001065","article-title":"Genome-Wide profiling of p63 DNA-Binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus","volume":"6","author":"Kouwenhoven","year":"2010","journal-title":"PLoS Genet."},{"key":"2023012512173119100_B6","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1038\/nrg2641","article-title":"ChIP-seq: advantages and challenges of a maturing technology","volume":"10","author":"Park","year":"2009","journal-title":"Nat. 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Biotech."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/270\/48868491\/bioinformatics_27_2_270.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/270\/48868491\/bioinformatics_27_2_270.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:54:00Z","timestamp":1674658440000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/2\/270\/285575"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,15]]},"references-count":9,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2011,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq636","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,1,15]]},"published":{"date-parts":[[2010,11,15]]}}}